I have had a good experience with the 256G ssd and various data drives. It is sufficient to get the OS loaded quickly and to store some games and media. I had done this with windows XP with an 80G ssd - and had to migrate many windows default directories to the standard HD. It worked, but was a bit messy.
Fundamentally - either choice is good - but for a good balance between storage and boot speed the two drives is a better solution in my opinion.
If you can afford it, then get the larger SSD. Everytime you access it, it saves you time.
However, if you plan on dumping lots of data onto it (like a music collection, videos, pictures, etc.) that won't be accessed very often, then you might be financially better off going with the 256GB SSD as primary & 1-4TB drive as 2nd drive for storage only.
If you know you can support the decision, one larger SSD is definitely the way to go. With that said, make backups. But if you need more than 1 TB, that's just not practical. Given the price of 512 GB-class drives like the EVO and Crucial M500, I think that's the way to go.